Yes, use flock. And strict, warnings and 3-argument open. Some sample locking code follows. Adjust according to your needs.
use strict;
use warnings;
use Fcntl ':flock'; # import LOCK_* constants
open(my $fhlock, '>', $somelockfile) or die "Error: open '$somelockfil
+e': $!";
# Note: process will block at this point until the lock is acquired.
flock($fhlock, LOCK_EX) or die "Error: flock '$somelockfile': $!";
# Lock is now held until $fhlock is closed.
# Note that even if this program crashes or is killed, $fhlock will
# be closed by the OS and the lock released.
# ...
# Release the lock simply by closing the file handle.
close $fhlock or die "Error: close '$somelockfile': $!";
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